Solutions (spoilers!) for Coursera Bioinformatics / Stepik Genome Sequencing course with Seq

I've always wanted to learn Bioinformatics / Genome Sequencing. Seq-lang's debut last week is the prefect catalyst for starting.

Seq seems like the perfect tool since it was created specifically for the job. The downside is that it is too young, so many features and "batteries" you expect from python, the language it is based on, are missing. In addition, the following some of the things I felt missing working on the problem set:

• functools
• better parse errors
• splat / unpack
• defaultdict

That being said, its speed, statical typing, pipeline operator |>, and similarities with python have made me overlook its early drawbacks easily.

1. Follow instructions to Install

2. Setup your editor to associate .seq as python.

3. Run via seqc FILE.seq ARG, eg.:

seqc stepik/1-1.seq 1   # run exercise 1 in stepik/1-1.seq
seqc stepik/1-1.seq 2-4 # run exercise 2-4 in stepik/1-1.seq
seqc stepik/1-1.seq     # run all exercises in stepik/1-1.seq

Not sure if

for kmr in dna.kmers[Kmer[4]](1):

is faster than

for kmr in dna.split(k, 1):

or not, but since Kmer[n] requires n to be a compile time constant, it' not too useful here.

abs(k1 - k2) # vs. len([1 for i in range(len(k1)) if k1[i] != k2[i]])

reversed=bool in .sort() or sorted(), so using [::-1]

lambda - Need to define and pass the function